[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/
commit: ca24f2e19942faa1d906b1716b7975458db3bd04 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 20 11:19:35 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 20 11:19:35 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca24f2e1 sci-biology/AlignGraph: fix MultipleKeywordsLines Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/AlignGraph/AlignGraph-.ebuild | 1 - 1 file changed, 1 deletion(-) diff --git a/sci-biology/AlignGraph/AlignGraph-.ebuild b/sci-biology/AlignGraph/AlignGraph-.ebuild index 60ea9d6b6..f48b436ee 100644 --- a/sci-biology/AlignGraph/AlignGraph-.ebuild +++ b/sci-biology/AlignGraph/AlignGraph-.ebuild @@ -11,7 +11,6 @@ HOMEPAGE="https://github.com/baoe/AlignGraph if [ "$PV" == "" ]; then inherit git-r3 EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git; - KEYWORDS="" else SRC_URI="" KEYWORDS=""
[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/
commit: a0c50cfcca14d8f8884a99ce9d6e95e601471475 Author: Andrew Ammerlaan riseup net> AuthorDate: Fri Mar 5 15:19:55 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Fri Mar 5 15:29:11 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0c50cfc sci-biology/AlignGraph: EAPI bump Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/AlignGraph/AlignGraph-.ebuild | 13 + 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/sci-biology/AlignGraph/AlignGraph-.ebuild b/sci-biology/AlignGraph/AlignGraph-.ebuild index 46d1029fd..60ea9d6b6 100644 --- a/sci-biology/AlignGraph/AlignGraph-.ebuild +++ b/sci-biology/AlignGraph/AlignGraph-.ebuild @@ -1,18 +1,15 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 inherit toolchain-funcs -if [ "$PV" == "" ]; then - inherit git-r3 -fi - DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads" HOMEPAGE="https://github.com/baoe/AlignGraph http://bioinformatics.oxfordjournals.org/content/30/12/i319.long; if [ "$PV" == "" ]; then + inherit git-r3 EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git; KEYWORDS="" else @@ -22,13 +19,13 @@ fi LICENSE="Artistic-2" SLOT="0" -IUSE="" DEPEND="" RDEPEND="${DEPEND} sci-biology/mummer sci-biology/blat - sci-biology/bowtie" + sci-biology/bowtie +" # AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both # need to be installed on the system. AlignGraph’s run time is currently 23–57 min
[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/
commit: 0da82a1a33fe2e91643dc2da891cfd5841417efe Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 23 15:06:01 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 23 15:06:01 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0da82a1a sci-biology/AlignGraph: improve DESCR; add mummer DEPEND Package-Manager: portage-2.2.28 sci-biology/AlignGraph/AlignGraph-.ebuild | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sci-biology/AlignGraph/AlignGraph-.ebuild b/sci-biology/AlignGraph/AlignGraph-.ebuild index 9754ee5..f6ea6bb 100644 --- a/sci-biology/AlignGraph/AlignGraph-.ebuild +++ b/sci-biology/AlignGraph/AlignGraph-.ebuild @@ -10,7 +10,7 @@ if [ "$PV" == "" ]; then inherit git-r3 fi -DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds" +DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads" HOMEPAGE="https://github.com/baoe/AlignGraph http://bioinformatics.oxfordjournals.org/content/30/12/i319.long; if [ "$PV" == "" ]; then @@ -27,6 +27,7 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} + sci-biology/mummer sci-biology/blat sci-biology/bowtie"
[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/
commit: add8084e363c64f4730fbee8ac16324401972495 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Apr 10 23:22:10 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Apr 10 23:22:10 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=add8084e sci-biology/AlignGraph: improve package DESCR Package-Manager: portage-2.2.28 sci-biology/AlignGraph/AlignGraph-.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/AlignGraph/AlignGraph-.ebuild b/sci-biology/AlignGraph/AlignGraph-.ebuild index 4a52cfd..9754ee5 100644 --- a/sci-biology/AlignGraph/AlignGraph-.ebuild +++ b/sci-biology/AlignGraph/AlignGraph-.ebuild @@ -10,7 +10,7 @@ if [ "$PV" == "" ]; then inherit git-r3 fi -DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence" +DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds" HOMEPAGE="https://github.com/baoe/AlignGraph http://bioinformatics.oxfordjournals.org/content/30/12/i319.long; if [ "$PV" == "" ]; then
[gentoo-commits] proj/sci:master commit in: sci-biology/AlignGraph/
commit: ab1f6781e9c576702f48058e7d9c86676973b693 Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Mon May 25 19:04:23 2015 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Mon May 25 19:04:23 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab1f6781 sci-biology/AlignGraph: new package Package-Manager: portage-2.2.18 sci-biology/AlignGraph/AlignGraph-.ebuild | 53 +++ sci-biology/AlignGraph/ChangeLog | 9 + sci-biology/AlignGraph/metadata.xml | 9 + 3 files changed, 71 insertions(+) diff --git a/sci-biology/AlignGraph/AlignGraph-.ebuild b/sci-biology/AlignGraph/AlignGraph-.ebuild new file mode 100644 index 000..b7e2866 --- /dev/null +++ b/sci-biology/AlignGraph/AlignGraph-.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +if [ $PV == ]; then + inherit git-r3 +fi + +DESCRIPTION=Asssemble contigs/scaffolds using related reference sequence +HOMEPAGE=https://github.com/baoe/AlignGraph + http://bioinformatics.oxfordjournals.org/content/30/12/i319.long; +if [ $PV == ]; then + EGIT_REPO_URI=https://github.com/baoe/AlignGraph.git; + KEYWORDS= +else + SRC_URI= + KEYWORDS= +fi + +LICENSE=Artistic-2 +SLOT=0 +IUSE= + +DEPEND= +RDEPEND=${DEPEND} + sci-biology/blat + sci-biology/bowtie + +# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both +# need to be installed on the system. AlignGraph’s run time is currently 23–57 min +# per million aligned reads. In the performance tests of this study, the memory usage +# was 36–50 GB, and it stays 100 GB even for entire mammalian genomes. These requirements +# are more moderate than those of most de novo assemblers (Luo et al., 2012). + +# 8 threads are hardcoded. Currently users cannot make changes to this, since this is +# a moderate choice for either single CPU machines (overhead for parallelization would +# not be too large) or multiple CPU machines. Another reason is, the bottleneck for the +# runtime is usually from BLAT, no matter how many threads there are for Bowtie2. +src_compile(){ + cd AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o AlignGraph AlignGraph.cpp -lpthread + cd ../Eval-AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o Eval-AlignGraph Eval-AlignGraph.cpp -lpthread +} + +src_install(){ + dobin AlignGraph/AlignGraph Eval-AlignGraph/Eval-AlignGraph + dodoc README.md +} diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog new file mode 100644 index 000..d6c0196 --- /dev/null +++ b/sci-biology/AlignGraph/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/AlignGraph +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*AlignGraph- (25 May 2015) + + 25 May 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz + +AlignGraph-.ebuild, +metadata.xml: + sci-biology/AlignGraph: new package diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml new file mode 100644 index 000..2bc8930 --- /dev/null +++ b/sci-biology/AlignGraph/metadata.xml @@ -0,0 +1,9 @@ +?xml version=1.0 encoding=UTF-8? +!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd; +pkgmetadata + herdsci-biology/herd + maintainer +emailmmokr...@fold.natur.cuni.cz/email +nameMartin Mokrejs/name + /maintainer +/pkgmetadata